The business-class airline will fly its final service between London Luton and New York Newark airport on September 24.
Customers due to travel beyond that date will either be eligible for a full refund or will have the option to rebook onto the airline’s Paris to New York route free of charge.
In a statement, the company said the decision had “not been taken lightly” and had been made “in view of a new economic climate in Europe... that has already affected various significant players within the airline industry”.
La Compagnie added that the UK’s vote to leave the EU in June “had played its part in long-term uncertainty for the airline industry”.
Due to the axing, the airline will now introduce a second daily flight from Paris to New York in October 2016.
“We would like to express our sincere thanks to each and every one of our passengers who have supported us since the launch of our London-New York operations from April 2015 to present," chief executive officer Frantz Yvelin added.
"This has not been an easy decision for us to make but we would like to emphasise that this is the suspension of, not the cancellation of, the London to New York route."